Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses

Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Rondebosch 7701, South Africa.
Journal of Virology (Impact Factor: 4.44). 01/2007; 80(23):11827-32. DOI: 10.1128/JVI.01100-06
Source: PubMed


Foot-and-mouth disease virus (FMDV) is thought to evolve largely through genetic drift driven by the inherently error-prone nature of its RNA polymerase.
There is, however, increasing evidence that recombination is an important mechanism in the evolution of these and other related
picornoviruses. Here, we use an extensive set of recombination detection methods to identify 86 unique potential recombination
events among 125 publicly available FMDV complete genome sequences. The large number of events detected between members of
different serotypes suggests that horizontal flow of sequences among the serotypes is relatively common and does not incur
severe fitness costs. Interestingly, the distribution of recombination breakpoints was found to be largely nonrandom. Whereas
there are clear breakpoint cold spots within the structural genes, two statistically significant hot spots precisely separate
these from the nonstructural genes. Very similar breakpoint distributions were found for other picornovirus species in the
genera Enterovirus and Teschovirus. Our results suggest that genome regions encoding the structural proteins of both FMDV and other picornaviruses are functionally
interchangeable modules, supporting recent proposals that the structural and nonstructural coding regions of the picornaviruses
are evolving largely independently of one another.

Download full-text


Available from: Arvind Varsani,
  • Source
    • "Because of the high mutation rate and saturation detected in cyt-b, we only used the 1st and 2nd codon positions when we used the full matrix. In all nuclear genes, recombination was tested using RDP: Recombination Detection Program v3.44 (Martin & Rybicki 2000; Heath et al. 2006). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The lizard genus Liolaemus and different clades within it have been the focus of several recent phylogenetic studies mainly based on morphology and mtDNA. Although there is general consensus for recognizing two clades (subgenera) within the genus, [Liolaemus (sensu stricto) and Eulaemus], phylogenetic relationships within each subgenus remain difficult to elucidate, given incomplete taxonomic sampling and large discordance between published studies. Here, new phylogenetic relationships for the Eulaemus subgenus are proposed based on the largest molecular data set ever used for this clade, which includes 188 individuals and 14 loci representing different parts of the genome (mtDNA, anonymous nuclear loci and nuclear protein-coding loci). This data set was analysed using two species tree approaches (*beast and MDC). Levels of discordance among methods were found, and with previously published studies, but results are robust enough to propose new phylogenetic hypotheses for the Eulaemus clade. Specifically well-resolved and well-supported novel hypotheses are provided within the lineomaculatus section, and we formally recognize the zullyae clade, the sarmientoi clade and the hatcheri group. We also resolve species relationships within the montanus section, and particularly within the melanops series. We found discordance between mitochondrial and nuclear trees and discussed alternative hypotheses for the lineomaculatus and montanus sections, as well as the challenge in resolving phylogenetic relationships for large clades in general.
    Zoologica Scripta 04/2014; 43(4). DOI:10.1111/zsc.12053 · 3.22 Impact Factor
  • Source
    • "Gene tree and species-tree analyses The best-fit evolutionary model for each gene (cyt-b [794 bp]: TRN+I+G; 12S [951 bp]: GTR+G; MXRA5 [961 bp]: TPM1lf+G, NKTR [1074 bp]: TRN+G, SIN- CAIP [449 bp]: TPM2 lf+G, RBMX [600 bp]: HKY+G, DMXL [959 bp]: HKY+G, ACA4 [1218 bp]: HKY+G, PLRL [543 bp]: TRN+G, Homo_30b [664 bp]: TIM1 + G, Homo_19b [642 bp]: HKY+G,) was selected using the corrected Akaike information criterion in JMODELTEST v0.1.1 (Posada 2008). For all nuclear genes, recombination was tested and excluded using RDP: Recombination Detection Program v3.44 (Martin & Rybicki 2000; Heath et al. 2006). Separate Bayesian analyses (BI) were conducted for each gene using MRBAYES v3.1.2 "
    [Show abstract] [Hide abstract]
    ABSTRACT: The genus Homonota was described by Gray (1845) and currently includes 10 species: Homonota andicola, H. borellii, H. darwinii, H. fasciata, H. rupicola, H. taragui, H. underwoodi, H. uruguayensis, H. williamsii & H. whitii and one subspecies of H. darwinii (H. darwinii macrocephala). It is distributed from 15° latitude south in southern Brazil, through much of Bolivia, Paraguay, Uruguay and Argentina to 54° south in Patagonia and across multiple different habitats. Several morphological taxonomic studies on a subset of these species have been published, but no molecular phylogenetic hypotheses are available for the genus. The objective of this study is to present a molecular phylogenetic hypothesis for all the described species in the genus. We sequenced two mitochondrial genes (cyt-b & 12S: 1745 bp), seven nuclear protein coding (RBMX, DMLX, NKTR, PLRL, SINCAIP, MXRA5, ACA4: 5804 bp) and two anonymous nuclear loci (30Hb, 19Hb: 1306 bp) and implemented traditional concatenated analyses (MP, ML, BI) as well as species-tree (*beast) approaches. All methods recovered almost the same topology. We recovered the genus Homonota as monophyletic with strong statistical support. Within Homonota, there are three strongly supported clades (whitii, borellii and fasciata), which differ from those previously proposed based on scale shape, osteology, myology and quantitative characters. Detailed morphological analyses based on this highly resolved and well-supported phylogeny will provide a framework for understanding morphological evolution and historical biogeography of this phenotypically conservative genus. We hypothesize that extensive marine transgressions during Middle and Late Miocene most probably isolated the ancestors of the three main clades in eastern Uruguay (borellii group), north-western Argentina-southern Bolivia (fasciata group), and central-western Argentina (whitii group). Phylogeographic and morphological/morphometric analyses coupled with paleo-niche modelling are needed to better understand its biogeographical history.
    Zoologica Scripta 03/2014; 43(3). DOI:10.1111/zsc.12052 · 3.22 Impact Factor
  • Source
    • "Haplotypes were inferred using PHASE (Stephens et al. 2001, Stephens and Donelly 2003), with an output threshold of 0.7, as implemented in DnaSP (Librado and Rozas 2009). Using RDP3, and seven inclusive tests in the program (Smith 1992, Padidam et al. 1999, Gibbs et al. 2000, Martin and Rybicki 2000, Posada and Crandall 2001, Martin et al. 2005, Heath et al. 2006, Boni et al. 2007), we checked for recombination. Using these tests, recombination was not detected in any of the Z-linked loci. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The properties of sex chromosomes, including patterns of inheritance, reduced levels of recombination, and hemizygosity in one of the sexes may result in the faster fixation of new mutations via drift and natural selection. Due to these patterns and processes, the two rules of speciation to describe the genetics of postzygotic isolation, Haldane's rule and the large-X effect, both explicitly include quicker evolution on sex chromosomes relative to autosomes. Because sex-linked mutations may be the first to become fixed in the speciation process, and appear to be due to stronger genetic drift (in birds), we may identify pronounced genetic differentiation in sex chromosomes in taxa experiencing recent speciation and diverging mainly via genetic drift. Here, we use nine sex-linked and 21 autosomal genetic markers to investigate differential divergence and introgression between marker types in Certhia americana. We identified increased levels of genetic differentiation and reduced levels of gene flow on sex chromosomes relative to autosomes. This pattern is similar to those observed in other recently-divergent avian species, providing another case study of the earlier role of sex chromosomes in divergence, relative to autosomes. Additionally, we identify three markers that may be under selection between Certhia americana lineages.
    Journal of Avian Biology 12/2013; 45(2). DOI:10.1111/j.1600-048X.2013.00233.x · 1.97 Impact Factor
Show more